[SOSlib-devel] [ sbmlsolver-Bugs-1924288 ] Only one timepoint

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Bugs item #1924288, was opened at 2008-03-24 13:23
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Category: solver malfunction
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Gabriel Plantat (gabrieljps)
Assigned to: Nobody/Anonymous (nobody)
Summary: Only one timepoint

Initial Comment:
Hello,
I have in fact two problems, and i think that i need the solution to only one of them :)
I'm trying to install the verison 1.6.0 on a Kubuntu (Linux) operating system. I have installed the libsbml.2.3.4 (compiled with the expat library) and sundials.2.3.0 libraries in a local directory, and when i compile the SBML_odeSolver, it crashes. I have set the --with-libsbml option to the directory where the libraries are, and it produces the error:

checking for SBML Library Version... expr: syntax error
expr: syntax error
expr: syntax error
./configure: line 4175: test: -eq: unary operator expected
configure: found SBML Library Version
checking correct functioning of SBML... yes
./configure: line 4278: test: -eq: unary operator expected
checking correct functioning of SUNDIALS CVODE... no:
                   CFLAGS=-g -O2 -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0//include
                   LDFLAGS= -L/home/gabrieljps/trabajos/synthbio2/genetdes_3.0//lib
                   LIBS= -lsundials_kinsol -lsundials_cvodes -lsundials_cvode -lsundials_nvecserial -lsundials_shared -lm
configure: error: Can not link to SUNDIALS CVODE Library



If i change the directory to where the files .so are (the same directory with a /lib appended), it gives this error:

checking for SBML Library Version... configure: found SBML Library Version 2.3.4
checking correct functioning of SBML... no:
                   CFLAGS=-g -O2 -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/include -I/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/include/sbml
                   LDFLAGS= -Wl,-rpath,/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/lib -L/home/gabrieljps/trabajos/synthbio2/genetdes_3.0/lib/lib
                   LIBS= -lxerces-c -lsbml
configure: error: Can not link to SBML Library:
                  Please, make sure to use libSBML version >= 2.3.2


So i began using the 1.6pre version, which compiles. But doesn't seem to be working properly. I have tried the integrate exemple file with the MAPK.xml file, and when i expect all the results from the integration, it just gives me one time. I have printed the results->timepoints variable and it is set to 1.
Even further, in this file the third parameter to be given is supposed to be the number of time steps, but if the number of steps is greater than the ending time, it crashes. On the contrary, if it is not, it doesn't, even if the number of steps is lower than 1 (0.1 for exemple)! 
Anyway, i have used the MAPK.xml file given as an exemple with the library, and i get only the initial conditions, and no other point of the integration.

I think that if i can integrate the function or intall the 1.6.0 version, i will have the problem solved. Thank you for your help!

Gabriel PLANTAT.
Ecole Polytechnique's student.
gab...@gm...


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